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Merge pull request #329 from ncbo/bugfix/property-label-resolution/326
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Fix property label rendering and code cleanup
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@jvendetti
jvendetti authored Sep 18, 2024
2 parents 297a6ba + 918eff1 commit 998ae8b
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Showing 4 changed files with 67 additions and 254 deletions.
213 changes: 67 additions & 146 deletions app/helpers/application_helper.rb
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Original file line number Diff line number Diff line change
@@ -1,40 +1,23 @@
# Methods added to this helper will be available to all templates in the application.

require 'uri'
require 'cgi'
require 'digest/sha1'
require 'pry' # used in a rescue

module ApplicationHelper

def get_apikey
unless session[:user].nil?
return session[:user].apikey
session[:user].apikey
else
return LinkedData::Client.settings.apikey
end
end

def isOwner?(id)
unless session[:user].nil?
if session[:user].admin?
return true
elsif session[:user].id.eql?(id)
return true
else
return false
end
LinkedData::Client.settings.apikey
end
end

def clean(string)
string = string.gsub("\"",'\'')
return string.gsub("\n",'')
string = string.gsub("\"", '\'')
string.gsub("\n", '')
end

def clean_id(string)
new_string = string.gsub(":","").gsub("-","_").gsub(".","_")
return new_string
string.gsub(':', '').gsub('-', '_').gsub('.', '_')
end

def get_username(user_id)
Expand All @@ -47,50 +30,31 @@ def current_user_admin?

def remove_owl_notation(string)
# TODO_REV: No OWL notation, but should we modify the IRI?
return string

unless string.nil?
strings = string.split(":")
if strings.size<2
#return string.titleize
return string
else
#return strings[1].titleize
return strings[1]
end
end
string
end

def draw_tree(root, id = nil, type = "Menu", submission)
def draw_tree(root, id = nil, type = 'Menu', submission)
if id.nil?
id = root.children.first.id
end
# TODO: handle tree view for obsolete classes, e.g. 'http://purl.obolibrary.org/obo/GO_0030400'
raw build_tree(root, "", id, submission) # returns a string, representing nested list items
raw build_tree(root, '', id, submission) # returns a string, representing nested list items
end

def build_tree(node, string, id, submission)
if node.children.nil? || node.children.length < 1
return string # unchanged
if node.children.nil? || node.children.empty?
return string
end

node.children.sort! {|a,b| (a.prefLabel || a.id).downcase <=> (b.prefLabel || b.id).downcase}
for child in node.children
if child.id.eql?(id)
active_style="class='active'"
else
active_style = ""
end
if child.expanded?
open = "class='open'"
else
open = ""
end
node.children.sort! { |a, b| (a.prefLabel || a.id).downcase <=> (b.prefLabel || b.id).downcase }
node.children.each do |child|
active_style = child.id.eql?(id) ? "class='active'" : ''
open = child.expanded? ? "class='open'" : ''

# This fake root will be present at the root of "flat" ontologies, we need to keep the id intact
li_id = child.id.eql?("bp_fake_root") ? "bp_fake_root" : short_uuid
li_id = child.id.eql?('bp_fake_root') ? 'bp_fake_root' : short_uuid

if child.id.eql?("bp_fake_root")
if child.id.eql?('bp_fake_root')
string << "<li class='active' id='#{li_id}'><a id='#{CGI.escape(child.id)}' href='#' #{active_style}>#{child.prefLabel}</a></li>"
else
icons = child.relation_icon(node)
Expand All @@ -99,23 +63,23 @@ def build_tree(node, string, id, submission)
if child.hasChildren && !child.expanded?
string << "<ul class='ajax'><li id='#{li_id}'><a id='#{CGI.escape(child.id)}' href='/ajax_concepts/#{child.explore.ontology.acronym}/?conceptid=#{CGI.escape(child.id)}&callback=children&lang=#{request_lang(submission)}'>ajax_class</a></li></ul>"
elsif child.expanded?
string << "<ul>"
string << '<ul>'
build_tree(child, string, id, submission)
string << "</ul>"
string << '</ul>'
end
string << "</li>"
string << '</li>'
end
end

string
end

def loading_spinner(padding = false, include_text = true)
loading_text = include_text ? " loading..." : ""
loading_text = include_text ? ' loading...' : ''
if padding
raw('<div style="padding: 1em;">' + image_tag("spinners/spinner_000000_16px.gif", style: "vertical-align: text-bottom;") + loading_text + '</div>')
raw('<div style="padding: 1em;">' + image_tag('spinners/spinner_000000_16px.gif', style: 'vertical-align: text-bottom;') + loading_text + '</div>')
else
raw(image_tag("spinners/spinner_000000_16px.gif", style: "vertical-align: text-bottom;") + loading_text)
raw(image_tag('spinners/spinner_000000_16px.gif', style: 'vertical-align: text-bottom;') + loading_text)
end
end

Expand All @@ -125,30 +89,11 @@ def short_uuid
rand(36**8).to_s(36)
end

def help_icon(link, html_attribs = {})
html_attribs["title"] ||= "Help"
attribs = []
html_attribs.each {|k,v| attribs << "#{k.to_s}='#{v}'"}
return <<-BLOCK
<a target="_blank" href='#{link}' class='pop_window help_link' #{attribs.join(" ")}>
<span class="pop_window ui-icon ui-icon-help"></span>
</a>
BLOCK
end

def anonymous_user
#
# TODO: Fix and failures from removing 'DataAccess' call here.
#
#user = DataAccess.getUser($ANONYMOUS_USER)
user ||= User.new({"id" => 0})
end

def render_advanced_picker(custom_ontologies = nil, selected_ontologies = [], align_to_dom_id = nil)
selected_ontologies ||= []
init_ontology_picker(custom_ontologies, selected_ontologies)
render :partial => "shared/ontology_picker_advanced", :locals => {
:custom_ontologies => custom_ontologies, :selected_ontologies => selected_ontologies, :align_to_dom_id => align_to_dom_id
render partial: 'shared/ontology_picker_advanced', locals: {
custom_ontologies: custom_ontologies, selected_ontologies: selected_ontologies, align_to_dom_id: align_to_dom_id
}
end

Expand All @@ -167,77 +112,71 @@ def init_ontology_picker_single
end

def get_ontologies_data(ontologies = nil)
ontologies ||= LinkedData::Client::Models::Ontology.all(include: "acronym,name")
ontologies ||= LinkedData::Client::Models::Ontology.all(include: 'acronym,name')
@onts_for_select = []
@onts_acronym_map = {}
@onts_uri2acronym_map = {}
ontologies.each do |ont|
# TODO: ontologies parameter may be a list of ontology models (not ontology submission models):
# ont.acronym instead of ont.ontology.acronym
# ont.name instead of ont.ontology.name
# ont.id instead of ont.ontology.id
# TODO: annotator passes in 'custom_ontologies' to the ontologies parameter.
next if ( ont.acronym.nil? or ont.acronym.empty? )
next if ont.acronym.blank?

acronym = ont.acronym
name = ont.name
#id = ont.id # ontology URI
abbreviation = acronym.empty? ? "" : "(#{acronym})"
abbreviation = acronym.empty? ? '' : "(#{acronym})"
ont_label = "#{name.strip} #{abbreviation}"
#@onts_for_select << [ont_label, id] # using the URI crashes the UI checkbox selection behavior.
@onts_for_select << [ont_label, acronym]
@onts_acronym_map[ont_label] = acronym
@onts_uri2acronym_map[ont.id] = acronym # required in ontologies_to_acronyms
@onts_uri2acronym_map[ont.id] = acronym
end
@onts_for_select.sort! { |a,b| a[0].downcase <=> b[0].downcase }
@onts_for_select.sort! { |a, b| a[0].downcase <=> b[0].downcase }
@onts_for_js = @onts_acronym_map.to_json
end

def categories_for_select
# This method is called in the search index page.
get_ontologies_data
get_categories_data
return @categories_for_select
@categories_for_select
end

def get_categories_data
@categories_for_select = []
@categories_map = {}
categories = LinkedData::Client::Models::Category.all(include: "name,ontologies")
categories = LinkedData::Client::Models::Category.all(include: 'name,ontologies')
categories.each do |c|
@categories_for_select << [ c.name, c.id ]
@categories_map[c.id] = ontologies_to_acronyms(c.ontologies) # c.ontologies is a list of URIs
@categories_for_select << [c.name, c.id]
@categories_map[c.id] = ontologies_to_acronyms(c.ontologies)
end
@categories_for_select.sort! { |a,b| a[0].downcase <=> b[0].downcase }
@categories_for_select.sort! { |a, b| a[0].downcase <=> b[0].downcase }
@categories_for_js = @categories_map.to_json
end

def get_groups_data
@groups_map = {}
@groups_for_select = []
groups = LinkedData::Client::Models::Group.all(include: "acronym,name,ontologies")
groups = LinkedData::Client::Models::Group.all(include: 'acronym,name,ontologies')
groups.each do |g|
next if ( g.acronym.nil? or g.acronym.empty? )
@groups_for_select << [ g.name + " (#{g.acronym})", g.acronym ]
@groups_map[g.acronym] = ontologies_to_acronyms(g.ontologies) # g.ontologies is a list of URIs
next if g.acronym.blank?

@groups_for_select << [g.name + " (#{g.acronym})", g.acronym]
@groups_map[g.acronym] = ontologies_to_acronyms(g.ontologies)
end
@groups_for_select.sort! { |a,b| a[0].downcase <=> b[0].downcase }
@groups_for_select.sort! { |a, b| a[0].downcase <=> b[0].downcase }
@groups_for_js = @groups_map.to_json
end

def ontologies_to_acronyms(ontologyIDs)
acronyms = []
ontologyIDs.each do |id|
acronyms << @onts_uri2acronym_map[id] # hash generated in get_ontologies_data
acronyms << @onts_uri2acronym_map[id]
end
return acronyms.compact # remove nil values from any failures to convert ontology URI to acronym
acronyms.compact
end

def at_slice?
!@subdomain_filter.nil? && !@subdomain_filter[:active].nil? && @subdomain_filter[:active] == true
end

def link_last_part(url)
return "" if url.nil?
return '' if url.nil?

if url.include?('#')
url.split('#').last
Expand All @@ -246,24 +185,13 @@ def link_last_part(url)
end
end

def truncate_with_more(text, options = {})
length ||= options[:length] ||= 30
trailing_text ||= options[:trailing_text] ||= " ... "
link_more ||= options[:link_more] ||= "[more]"
link_less ||= options[:link_less] ||= "[less]"
more_text = " <a href='javascript:void(0);' class='truncated_more'>#{link_more}</a></span><span class='truncated_less'>#{text} <a href='javascript:void(0);' class='truncated_less'>#{link_less}</a></span>"
more = text.length > length ? more_text : "</span>"
output = "<span class='more_less_container'><span class='truncated_more'>#{truncate(text, :length => length, :omission => trailing_text)}" + more + "</span>"
end

def subscribe_ontology_button(ontology_id, user = nil)
user = session[:user] if user.nil?
if user.nil?
# subscribe button must redirect to login
return sanitize("<a href='/login?redirect=#{request.url}' style='font-size: .9em;' class='subscribe_to_ontology'>Subscribe</a>")
end
# Init subscribe button parameters.
sub_text = "Subscribe"

sub_text = 'Subscribe'
params = "data-bp_ontology_id='#{ontology_id}' data-bp_is_subbed='false' data-bp_user_id='#{user.id}'"
begin
# Try to create an intelligent subscribe button.
Expand All @@ -272,17 +200,15 @@ def subscribe_ontology_button(ontology_id, user = nil)
else
ont = LinkedData::Client::Models::Ontology.find_by_acronym(ontology_id).first
end
subscribed = subscribed_to_ontology?(ont.acronym, user) # application_helper
sub_text = subscribed ? "Unsubscribe" : "Subscribe"
subscribed = subscribed_to_ontology?(ont.acronym, user)
sub_text = subscribed ? 'Unsubscribe' : 'Subscribe'
params = "data-bp_ontology_id='#{ont.acronym}' data-bp_is_subbed='#{subscribed}' data-bp_user_id='#{user.id}'"
rescue
# pass, fallback init done above begin block to scope parameters beyond the begin/rescue block
end
# TODO: modify/copy CSS for notes_sub_error => subscribe_error
# TODO: modify/copy CSS for subscribe_to_notes => subscribe_to_ontology
spinner = '<span class="subscribe_spinner" style="display: none;">' + image_tag("spinners/spinner_000000_16px.gif", style: "vertical-align: text-bottom;") + '</span>'
error = "<span style='color: red;' class='subscribe_error'></span>"
return "<a href='javascript:void(0);' class='subscribe_to_ontology link_button' #{params}>#{sub_text}</a> #{spinner} #{error}"
"<a href='javascript:void(0);' class='subscribe_to_ontology link_button' #{params}>#{sub_text}</a> #{spinner} #{error}"
end

def subscribed_to_ontology?(ontology_acronym, user)
Expand All @@ -305,10 +231,11 @@ def ontolobridge_instructions_template(ontology)

# http://stackoverflow.com/questions/1293573/rails-smart-text-truncation
def smart_truncate(s, opts = {})
opts = {:words => 20}.merge(opts)
opts = { words: 20 }.merge(opts)
if opts[:sentences]
return s.split(/\.(\s|$)+/)[0, opts[:sentences]].map{|s| s.strip}.join('. ') + '. ...'
return s.split(/\.(\s|$)+/)[0, opts[:sentences]].map { |s| s.strip }.join('. ') + '. ...'
end

a = s.split(/\s/) # or /[ ]+/ to only split on spaces
n = opts[:words]
a[0...n].join(' ') + (a.size > n ? '...' : '')
Expand All @@ -319,11 +246,9 @@ def smart_truncate(s, opts = {})
# => '06/27/2010'
def xmldatetime_to_date(xml_date_time_str)
require 'date'
d = DateTime.xmlschema( xml_date_time_str ).to_date
d = DateTime.xmlschema(xml_date_time_str).to_date
# Return conventional US date format:
return sprintf("%02d/%02d/%4d", d.month, d.day, d.year)
# Or return "yyyy/mm/dd" format with:
#return DateTime.xmlschema( xml_date_time_str ).to_date.to_s
sprintf("%02d/%02d/%4d", d.month, d.day, d.year)
end

def flash_class(level)
Expand All @@ -337,41 +262,37 @@ def flash_class(level)
bootstrap_alert_class[level]
end

###BEGIN ruby equivalent of JS code in bp_ajax_controller.
###Note: this code is used in concepts/_details partial.
# NOTE: The following 4 methods (bp_ont_link, bp_class_link, get_link_for_cls_ajax, get_link_for_ont_ajax) are
# the Ruby equivalent of JS code in bp_ajax_controller.js and are used in the concepts/_details partial.
def bp_ont_link(ont_acronym)
return "/ontologies/#{ont_acronym}"
"/ontologies/#{ont_acronym}"
end

def bp_class_link(cls_id, ont_acronym)
ontology_path(id: ont_acronym, p: 'classes', conceptid: cls_id)
end

def get_link_for_cls_ajax(cls_id, ont_acronym, target=nil)
# Note: bp_ajax_controller.ajax_process_cls will try to resolve class labels.
def get_link_for_cls_ajax(cls_id, ont_acronym, target = nil)
# NOTE: bp_ajax_controller.ajax_process_cls will try to resolve class labels.
# Uses 'http' as a more generic attempt to resolve class labels than .include? ont_acronym; the
# bp_ajax_controller.ajax_process_cls will try to resolve class labels and
# otherwise remove the UNIQUE_SPLIT_STR and the ont_acronym.
if target.nil?
target = ""
else
target = " target='#{target}' "
end
if cls_id.start_with? 'http://'
target = target.nil? ? '' : " target='#{target}' "

if cls_id.start_with?('http://', 'https://')
href_cls = " href='#{bp_class_link(cls_id, ont_acronym)}' "
data_cls = " data-cls='#{cls_id}' "
data_ont = " data-ont='#{ont_acronym}' "
return "<a class='cls4ajax' #{data_ont} #{data_cls} #{href_cls} #{target}>#{cls_id}</a>"
"<a class='cls4ajax' #{data_ont} #{data_cls} #{href_cls} #{target}>#{cls_id}</a>"
else
return auto_link(cls_id, :all, :target => '_blank')
auto_link(cls_id, :all, target: '_blank')
end
end

def get_link_for_ont_ajax(ont_acronym)
# ajax call will replace the acronym with an ontology name (triggered by class='ont4ajax')
# Ajax call will replace the acronym with an ontology name (triggered by class='ont4ajax')
href_ont = " href='#{bp_ont_link(ont_acronym)}' "
data_ont = " data-ont='#{ont_acronym}' "
return "<a class='ont4ajax' #{data_ont} #{href_ont}>#{ont_acronym}</a>"
"<a class='ont4ajax' #{data_ont} #{href_ont}>#{ont_acronym}</a>"
end
###END ruby equivalent of JS code in bp_ajax_controller.

end
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